Starting phenix.real_space_refine on Mon Dec 30 05:20:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gck_51231/12_2024/9gck_51231.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gck_51231/12_2024/9gck_51231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gck_51231/12_2024/9gck_51231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gck_51231/12_2024/9gck_51231.map" model { file = "/net/cci-nas-00/data/ceres_data/9gck_51231/12_2024/9gck_51231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gck_51231/12_2024/9gck_51231.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 90 5.49 5 S 41 5.16 5 C 7590 2.51 5 N 2092 2.21 5 O 2485 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12298 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3491 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 13, 'TRANS': 415} Chain: "B" Number of atoms: 2443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2443 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 6, 'TRANS': 287} Chain: "C" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1823 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 20, 'TRANS': 210} Chain: "D" Number of atoms: 2696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2696 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 309} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 900 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain: "F" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 945 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Time building chain proxies: 7.49, per 1000 atoms: 0.61 Number of scatterers: 12298 At special positions: 0 Unit cell: (89.598, 116.724, 160.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 41 16.00 P 90 15.00 O 2485 8.00 N 2092 7.00 C 7590 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.20 Conformation dependent library (CDL) restraints added in 1.5 seconds 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2460 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 5 sheets defined 50.4% alpha, 7.7% beta 33 base pairs and 87 stacking pairs defined. Time for finding SS restraints: 4.71 Creating SS restraints... Processing helix chain 'A' and resid 739 through 758 removed outlier: 4.211A pdb=" N GLN A 744 " --> pdb=" O LYS A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 766 Processing helix chain 'A' and resid 767 through 769 No H-bonds generated for 'chain 'A' and resid 767 through 769' Processing helix chain 'A' and resid 773 through 809 removed outlier: 6.192A pdb=" N HIS A 790 " --> pdb=" O VAL A 786 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N SER A 791 " --> pdb=" O ARG A 787 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A 794 " --> pdb=" O HIS A 790 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ALA A 795 " --> pdb=" O SER A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 820 removed outlier: 3.598A pdb=" N VAL A 818 " --> pdb=" O SER A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 838 Processing helix chain 'A' and resid 847 through 855 Processing helix chain 'A' and resid 874 through 885 Processing helix chain 'A' and resid 897 through 916 removed outlier: 4.039A pdb=" N SER A 903 " --> pdb=" O SER A 899 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N TYR A 906 " --> pdb=" O GLN A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 927 removed outlier: 4.146A pdb=" N GLU A 927 " --> pdb=" O ARG A 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 923 through 927' Processing helix chain 'A' and resid 933 through 947 Processing helix chain 'A' and resid 961 through 971 Processing helix chain 'A' and resid 972 through 991 removed outlier: 3.882A pdb=" N PHE A 976 " --> pdb=" O ASN A 972 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N CYS A 984 " --> pdb=" O PHE A 980 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU A 989 " --> pdb=" O LYS A 985 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU A 991 " --> pdb=" O ASN A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1016 removed outlier: 4.557A pdb=" N ASP A1012 " --> pdb=" O TRP A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1046 removed outlier: 3.660A pdb=" N LEU A1045 " --> pdb=" O ILE A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1105 removed outlier: 4.265A pdb=" N PHE A1104 " --> pdb=" O ASN A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1117 removed outlier: 3.668A pdb=" N LEU A1113 " --> pdb=" O THR A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1136 removed outlier: 4.536A pdb=" N GLU A1128 " --> pdb=" O HIS A1124 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A1129 " --> pdb=" O GLU A1125 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP A1132 " --> pdb=" O GLU A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1145 No H-bonds generated for 'chain 'A' and resid 1143 through 1145' Processing helix chain 'B' and resid 733 through 747 Processing helix chain 'B' and resid 752 through 765 removed outlier: 3.502A pdb=" N VAL B 758 " --> pdb=" O ASP B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 770 Processing helix chain 'B' and resid 771 through 787 removed outlier: 3.533A pdb=" N LEU B 787 " --> pdb=" O LEU B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 804 removed outlier: 3.714A pdb=" N ASN B 804 " --> pdb=" O ARG B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 820 Processing helix chain 'B' and resid 823 through 825 No H-bonds generated for 'chain 'B' and resid 823 through 825' Processing helix chain 'B' and resid 826 through 832 removed outlier: 3.785A pdb=" N LEU B 830 " --> pdb=" O SER B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 852 removed outlier: 3.774A pdb=" N PHE B 838 " --> pdb=" O ILE B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 887 removed outlier: 4.131A pdb=" N ILE B 880 " --> pdb=" O TYR B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 903 removed outlier: 3.851A pdb=" N TYR B 897 " --> pdb=" O SER B 893 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 924 removed outlier: 3.774A pdb=" N ASN B 912 " --> pdb=" O ASP B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 930 through 953 removed outlier: 3.507A pdb=" N HIS B 937 " --> pdb=" O PHE B 933 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY B 938 " --> pdb=" O GLN B 934 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR B 941 " --> pdb=" O HIS B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 957 Processing helix chain 'B' and resid 958 through 972 Processing helix chain 'B' and resid 974 through 988 removed outlier: 3.749A pdb=" N TYR B 981 " --> pdb=" O ILE B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 1009 removed outlier: 3.915A pdb=" N HIS B 997 " --> pdb=" O LYS B 993 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE B1005 " --> pdb=" O ASN B1001 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN B1008 " --> pdb=" O ILE B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1011 through 1023 Processing helix chain 'C' and resid 48 through 59 removed outlier: 4.066A pdb=" N LYS C 54 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N CYS C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 71 removed outlier: 4.176A pdb=" N LYS C 64 " --> pdb=" O GLY C 60 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS C 66 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE C 69 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS C 70 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU C 71 " --> pdb=" O GLU C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 129 Processing helix chain 'C' and resid 132 through 139 Processing helix chain 'C' and resid 173 through 183 Processing helix chain 'C' and resid 187 through 196 removed outlier: 5.185A pdb=" N SER C 193 " --> pdb=" O ASN C 189 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE C 194 " --> pdb=" O ASN C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'D' and resid 14 through 18 Processing helix chain 'D' and resid 37 through 54 removed outlier: 3.562A pdb=" N LEU D 54 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 81 removed outlier: 3.597A pdb=" N LEU D 70 " --> pdb=" O PHE D 66 " (cutoff:3.500A) Proline residue: D 75 - end of helix removed outlier: 3.813A pdb=" N LYS D 78 " --> pdb=" O GLN D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 91 Processing helix chain 'D' and resid 107 through 115 removed outlier: 4.435A pdb=" N LYS D 113 " --> pdb=" O GLU D 109 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE D 114 " --> pdb=" O ILE D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 158 Proline residue: D 148 - end of helix removed outlier: 3.520A pdb=" N LYS D 156 " --> pdb=" O GLU D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 182 removed outlier: 3.603A pdb=" N LEU D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 354 Processing sheet with id=AA1, first strand: chain 'A' and resid 858 through 860 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 858 through 860 current: chain 'C' and resid 103 through 107 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 103 through 107 current: chain 'C' and resid 147 through 162 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 147 through 162 current: chain 'D' and resid 328 through 331 removed outlier: 4.396A pdb=" N LEU D 335 " --> pdb=" O VAL D 432 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU D 337 " --> pdb=" O SER D 430 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LYS D 424 " --> pdb=" O LEU D 343 " (cutoff:3.500A) removed outlier: 10.844A pdb=" N GLY D 345 " --> pdb=" O ARG D 422 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N ARG D 422 " --> pdb=" O GLY D 345 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 920 through 922 Processing sheet with id=AA3, first strand: chain 'A' and resid 997 through 998 Processing sheet with id=AA4, first strand: chain 'A' and resid 1139 through 1141 Processing sheet with id=AA5, first strand: chain 'D' and resid 119 through 120 removed outlier: 6.326A pdb=" N VAL D 84 " --> pdb=" O SER D 120 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA D 61 " --> pdb=" O TYR D 85 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LYS D 206 " --> pdb=" O ASN D 241 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ASN D 241 " --> pdb=" O LYS D 206 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N GLU D 208 " --> pdb=" O THR D 239 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N THR D 239 " --> pdb=" O GLU D 208 " (cutoff:3.500A) 431 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 87 stacking parallelities Total time for adding SS restraints: 4.55 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1985 1.32 - 1.46: 3902 1.46 - 1.61: 6685 1.61 - 1.75: 105 1.75 - 1.89: 72 Bond restraints: 12749 Sorted by residual: bond pdb=" CA SER A1076 " pdb=" CB SER A1076 " ideal model delta sigma weight residual 1.530 1.443 0.086 1.69e-02 3.50e+03 2.61e+01 bond pdb=" C VAL A1080 " pdb=" O VAL A1080 " ideal model delta sigma weight residual 1.238 1.182 0.056 1.10e-02 8.26e+03 2.59e+01 bond pdb=" C TYR B1000 " pdb=" O TYR B1000 " ideal model delta sigma weight residual 1.236 1.178 0.058 1.15e-02 7.56e+03 2.55e+01 bond pdb=" N VAL D 104 " pdb=" CA VAL D 104 " ideal model delta sigma weight residual 1.454 1.493 -0.039 7.70e-03 1.69e+04 2.54e+01 bond pdb=" C ASN B 964 " pdb=" O ASN B 964 " ideal model delta sigma weight residual 1.237 1.180 0.057 1.16e-02 7.43e+03 2.40e+01 ... (remaining 12744 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 13894 2.31 - 4.62: 3344 4.62 - 6.93: 367 6.93 - 9.24: 21 9.24 - 11.55: 6 Bond angle restraints: 17632 Sorted by residual: angle pdb=" CA PHE B 933 " pdb=" CB PHE B 933 " pdb=" CG PHE B 933 " ideal model delta sigma weight residual 113.80 124.03 -10.23 1.00e+00 1.00e+00 1.05e+02 angle pdb=" C4' DT E 30 " pdb=" C3' DT E 30 " pdb=" O3' DT E 30 " ideal model delta sigma weight residual 110.00 99.28 10.72 1.50e+00 4.44e-01 5.11e+01 angle pdb=" CA ASN B 964 " pdb=" CB ASN B 964 " pdb=" CG ASN B 964 " ideal model delta sigma weight residual 112.60 105.87 6.73 1.00e+00 1.00e+00 4.53e+01 angle pdb=" C LEU C 140 " pdb=" N LYS C 141 " pdb=" CA LYS C 141 " ideal model delta sigma weight residual 120.38 129.13 -8.75 1.37e+00 5.33e-01 4.08e+01 angle pdb=" C ASN C 44 " pdb=" CA ASN C 44 " pdb=" CB ASN C 44 " ideal model delta sigma weight residual 112.07 121.26 -9.19 1.48e+00 4.57e-01 3.85e+01 ... (remaining 17627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 6066 17.93 - 35.86: 963 35.86 - 53.79: 355 53.79 - 71.72: 198 71.72 - 89.65: 10 Dihedral angle restraints: 7592 sinusoidal: 3794 harmonic: 3798 Sorted by residual: dihedral pdb=" CA LEU D 343 " pdb=" C LEU D 343 " pdb=" N VAL D 344 " pdb=" CA VAL D 344 " ideal model delta harmonic sigma weight residual 180.00 147.73 32.27 0 5.00e+00 4.00e-02 4.17e+01 dihedral pdb=" CA ARG C 35 " pdb=" C ARG C 35 " pdb=" N ILE C 36 " pdb=" CA ILE C 36 " ideal model delta harmonic sigma weight residual -180.00 -148.21 -31.79 0 5.00e+00 4.00e-02 4.04e+01 dihedral pdb=" CA TYR C 242 " pdb=" C TYR C 242 " pdb=" N LYS C 243 " pdb=" CA LYS C 243 " ideal model delta harmonic sigma weight residual 180.00 148.55 31.45 0 5.00e+00 4.00e-02 3.96e+01 ... (remaining 7589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 1610 0.128 - 0.255: 250 0.255 - 0.383: 43 0.383 - 0.510: 52 0.510 - 0.638: 2 Chirality restraints: 1957 Sorted by residual: chirality pdb=" P DA F 1 " pdb=" OP1 DA F 1 " pdb=" OP2 DA F 1 " pdb=" O5' DA F 1 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" P DT E 1 " pdb=" OP1 DT E 1 " pdb=" OP2 DT E 1 " pdb=" O5' DT E 1 " both_signs ideal model delta sigma weight residual True 2.35 -2.97 -0.62 2.00e-01 2.50e+01 9.67e+00 chirality pdb=" P DT E 28 " pdb=" OP1 DT E 28 " pdb=" OP2 DT E 28 " pdb=" O5' DT E 28 " both_signs ideal model delta sigma weight residual True 2.35 -2.85 -0.50 2.00e-01 2.50e+01 6.29e+00 ... (remaining 1954 not shown) Planarity restraints: 1931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 943 " 0.126 2.00e-02 2.50e+03 7.04e-02 9.91e+01 pdb=" CG TYR B 943 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR B 943 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR B 943 " -0.056 2.00e-02 2.50e+03 pdb=" CE1 TYR B 943 " -0.048 2.00e-02 2.50e+03 pdb=" CE2 TYR B 943 " -0.025 2.00e-02 2.50e+03 pdb=" CZ TYR B 943 " -0.027 2.00e-02 2.50e+03 pdb=" OH TYR B 943 " 0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 886 " 0.095 2.00e-02 2.50e+03 4.88e-02 4.76e+01 pdb=" CG TYR B 886 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TYR B 886 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR B 886 " -0.047 2.00e-02 2.50e+03 pdb=" CE1 TYR B 886 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 886 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 886 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR B 886 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 963 " -0.094 2.00e-02 2.50e+03 4.85e-02 4.70e+01 pdb=" CG TYR B 963 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 TYR B 963 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR B 963 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR B 963 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR B 963 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR B 963 " -0.016 2.00e-02 2.50e+03 pdb=" OH TYR B 963 " -0.046 2.00e-02 2.50e+03 ... (remaining 1928 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 33 2.54 - 3.13: 9360 3.13 - 3.72: 20085 3.72 - 4.31: 30106 4.31 - 4.90: 45890 Nonbonded interactions: 105474 Sorted by model distance: nonbonded pdb=" NZ LYS B 811 " pdb=" O SER C 197 " model vdw 1.954 3.120 nonbonded pdb=" OG SER C 38 " pdb=" OE2 GLU D 347 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR B 879 " pdb=" O PRO C 228 " model vdw 2.276 3.040 nonbonded pdb=" NE2 GLN B 814 " pdb=" O GLN C 226 " model vdw 2.280 3.120 nonbonded pdb=" OD1 ASN A1054 " pdb=" NZ LYS B 947 " model vdw 2.286 3.120 ... (remaining 105469 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.210 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.091 12749 Z= 0.922 Angle : 1.892 11.545 17632 Z= 1.274 Chirality : 0.122 0.638 1957 Planarity : 0.010 0.153 1931 Dihedral : 21.024 89.645 5132 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.03 % Favored : 94.74 % Rotamer: Outliers : 0.77 % Allowed : 3.33 % Favored : 95.90 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.21), residues: 1273 helix: -2.43 (0.16), residues: 547 sheet: -0.46 (0.56), residues: 64 loop : -1.23 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.012 TRP A1153 HIS 0.027 0.005 HIS A1151 PHE 0.055 0.009 PHE D 350 TYR 0.126 0.014 TYR B 943 ARG 0.028 0.002 ARG A 923 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 203 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 803 MET cc_start: 0.6571 (mtm) cc_final: 0.5509 (ttp) REVERT: A 1033 LEU cc_start: 0.8015 (mp) cc_final: 0.7518 (tp) REVERT: A 1040 PHE cc_start: 0.6134 (t80) cc_final: 0.5763 (t80) REVERT: A 1045 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6537 (tt) REVERT: A 1068 LYS cc_start: 0.9081 (mptt) cc_final: 0.8732 (tmtt) REVERT: A 1069 VAL cc_start: 0.7888 (t) cc_final: 0.7647 (t) REVERT: A 1097 MET cc_start: 0.9627 (ttp) cc_final: 0.9303 (tmm) REVERT: B 740 MET cc_start: 0.6936 (mmp) cc_final: 0.6433 (mmt) REVERT: B 777 MET cc_start: 0.5755 (ttm) cc_final: 0.5471 (ttt) REVERT: B 793 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8652 (tm-30) REVERT: B 870 ASN cc_start: 0.9605 (m-40) cc_final: 0.9337 (t0) REVERT: B 871 LYS cc_start: 0.8782 (mttt) cc_final: 0.8354 (ptmm) REVERT: B 910 MET cc_start: 0.7625 (mmm) cc_final: 0.7204 (mmm) REVERT: C 79 HIS cc_start: 0.8358 (m-70) cc_final: 0.7978 (m90) REVERT: C 116 ILE cc_start: 0.8724 (mt) cc_final: 0.8512 (mm) REVERT: C 204 GLN cc_start: 0.9396 (mt0) cc_final: 0.9107 (mm-40) REVERT: C 233 LEU cc_start: 0.8461 (mt) cc_final: 0.8212 (mt) REVERT: D 55 ASP cc_start: 0.8666 (m-30) cc_final: 0.8384 (m-30) REVERT: D 141 MET cc_start: 0.8862 (mmm) cc_final: 0.8579 (mtt) REVERT: D 204 LEU cc_start: 0.6800 (tp) cc_final: 0.6393 (tp) REVERT: D 239 THR cc_start: 0.2250 (p) cc_final: 0.1807 (p) REVERT: D 323 GLU cc_start: 0.8586 (pm20) cc_final: 0.8254 (mp0) outliers start: 9 outliers final: 3 residues processed: 211 average time/residue: 0.3318 time to fit residues: 93.3737 Evaluate side-chains 134 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 130 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1128 GLU Chi-restraints excluded: chain B residue 836 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 20.0000 chunk 102 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 78 optimal weight: 0.4980 chunk 122 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 987 ASN ** A1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12749 Z= 0.265 Angle : 0.766 8.100 17632 Z= 0.426 Chirality : 0.045 0.237 1957 Planarity : 0.005 0.051 1931 Dihedral : 22.831 79.223 2494 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.59 % Favored : 97.33 % Rotamer: Outliers : 1.96 % Allowed : 8.79 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.22), residues: 1273 helix: -0.59 (0.20), residues: 569 sheet: -0.16 (0.53), residues: 85 loop : -0.69 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 800 HIS 0.010 0.001 HIS B 919 PHE 0.034 0.002 PHE B 839 TYR 0.034 0.002 TYR B1000 ARG 0.007 0.001 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 757 LYS cc_start: 0.8396 (tttt) cc_final: 0.8130 (tptp) REVERT: A 803 MET cc_start: 0.6042 (mtm) cc_final: 0.5212 (ttt) REVERT: A 826 LEU cc_start: 0.9049 (mm) cc_final: 0.8567 (pp) REVERT: A 830 TRP cc_start: 0.8355 (t60) cc_final: 0.8152 (t60) REVERT: A 833 PHE cc_start: 0.9206 (m-80) cc_final: 0.8738 (m-80) REVERT: A 872 MET cc_start: 0.5378 (mtm) cc_final: 0.4231 (mtm) REVERT: A 1018 LEU cc_start: 0.7454 (mp) cc_final: 0.6740 (tp) REVERT: A 1040 PHE cc_start: 0.5614 (t80) cc_final: 0.4952 (t80) REVERT: A 1045 LEU cc_start: 0.6378 (OUTLIER) cc_final: 0.5661 (tp) REVERT: A 1068 LYS cc_start: 0.9109 (mptt) cc_final: 0.8729 (pptt) REVERT: A 1069 VAL cc_start: 0.7664 (t) cc_final: 0.7407 (m) REVERT: B 740 MET cc_start: 0.6641 (mmp) cc_final: 0.5995 (mmm) REVERT: B 793 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8570 (pp20) REVERT: B 870 ASN cc_start: 0.9509 (m-40) cc_final: 0.9297 (t0) REVERT: B 871 LYS cc_start: 0.8833 (mttt) cc_final: 0.8430 (pttp) REVERT: C 79 HIS cc_start: 0.8154 (m-70) cc_final: 0.7767 (m90) REVERT: C 204 GLN cc_start: 0.8842 (mt0) cc_final: 0.8628 (mp10) REVERT: C 235 MET cc_start: 0.4315 (mmm) cc_final: 0.3971 (mmm) REVERT: D 158 TYR cc_start: 0.7637 (m-80) cc_final: 0.7158 (m-80) REVERT: D 188 MET cc_start: -0.0985 (mmm) cc_final: -0.2500 (tpt) REVERT: D 323 GLU cc_start: 0.8681 (pm20) cc_final: 0.8235 (mp0) outliers start: 23 outliers final: 9 residues processed: 163 average time/residue: 0.2956 time to fit residues: 66.8192 Evaluate side-chains 125 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 781 TRP Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain B residue 836 GLN Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 297 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 33 optimal weight: 0.0970 chunk 122 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 chunk 121 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 877 GLN ** A1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 836 GLN B 959 GLN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12749 Z= 0.251 Angle : 0.690 7.528 17632 Z= 0.381 Chirality : 0.043 0.216 1957 Planarity : 0.004 0.054 1931 Dihedral : 22.837 67.458 2487 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.75 % Favored : 97.17 % Rotamer: Outliers : 2.56 % Allowed : 11.09 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.23), residues: 1273 helix: -0.14 (0.21), residues: 572 sheet: -0.04 (0.55), residues: 83 loop : -0.54 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 800 HIS 0.011 0.001 HIS B 919 PHE 0.023 0.002 PHE B 839 TYR 0.031 0.002 TYR B1000 ARG 0.005 0.001 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 803 MET cc_start: 0.6075 (mtm) cc_final: 0.4920 (ttt) REVERT: A 826 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8598 (pp) REVERT: A 833 PHE cc_start: 0.9258 (m-80) cc_final: 0.8834 (m-80) REVERT: A 949 GLN cc_start: 0.8702 (mp10) cc_final: 0.8274 (tp-100) REVERT: A 1033 LEU cc_start: 0.7911 (mp) cc_final: 0.7561 (mt) REVERT: A 1040 PHE cc_start: 0.5806 (t80) cc_final: 0.5292 (t80) REVERT: A 1045 LEU cc_start: 0.5829 (OUTLIER) cc_final: 0.5298 (tp) REVERT: A 1068 LYS cc_start: 0.9148 (mptt) cc_final: 0.8768 (tmtt) REVERT: A 1104 PHE cc_start: 0.8390 (m-80) cc_final: 0.7789 (m-80) REVERT: B 740 MET cc_start: 0.6318 (mmp) cc_final: 0.5845 (mmm) REVERT: B 793 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8533 (pp20) REVERT: B 870 ASN cc_start: 0.9490 (m-40) cc_final: 0.9280 (t0) REVERT: B 871 LYS cc_start: 0.8797 (mttt) cc_final: 0.8348 (pttp) REVERT: C 79 HIS cc_start: 0.8115 (m-70) cc_final: 0.7751 (m90) REVERT: C 116 ILE cc_start: 0.8444 (mm) cc_final: 0.8237 (mm) REVERT: D 141 MET cc_start: 0.8654 (mtt) cc_final: 0.8309 (mmm) REVERT: D 158 TYR cc_start: 0.7546 (m-80) cc_final: 0.7082 (m-80) REVERT: D 188 MET cc_start: -0.0871 (mmm) cc_final: -0.1852 (tpt) REVERT: D 323 GLU cc_start: 0.8741 (pm20) cc_final: 0.8284 (mp0) outliers start: 30 outliers final: 14 residues processed: 151 average time/residue: 0.2983 time to fit residues: 62.6987 Evaluate side-chains 124 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain B residue 836 GLN Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 1017 HIS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 297 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 13 optimal weight: 30.0000 chunk 58 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 959 GLN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 12749 Z= 0.281 Angle : 0.687 7.743 17632 Z= 0.375 Chirality : 0.043 0.237 1957 Planarity : 0.005 0.057 1931 Dihedral : 22.995 69.871 2487 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.14 % Favored : 96.78 % Rotamer: Outliers : 2.47 % Allowed : 13.82 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.23), residues: 1273 helix: -0.22 (0.21), residues: 578 sheet: -0.30 (0.57), residues: 81 loop : -0.55 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 93 HIS 0.011 0.001 HIS B 919 PHE 0.028 0.002 PHE D 150 TYR 0.029 0.002 TYR B1000 ARG 0.009 0.001 ARG A 784 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 803 MET cc_start: 0.6118 (mtm) cc_final: 0.4916 (ttt) REVERT: A 826 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8608 (pp) REVERT: A 833 PHE cc_start: 0.9313 (m-80) cc_final: 0.8922 (m-80) REVERT: A 872 MET cc_start: 0.5675 (mtm) cc_final: 0.5120 (mtp) REVERT: A 1040 PHE cc_start: 0.6327 (t80) cc_final: 0.5741 (t80) REVERT: A 1045 LEU cc_start: 0.5848 (OUTLIER) cc_final: 0.5270 (tp) REVERT: A 1068 LYS cc_start: 0.9196 (mptt) cc_final: 0.8824 (tmmt) REVERT: A 1104 PHE cc_start: 0.8429 (m-80) cc_final: 0.7932 (m-80) REVERT: A 1135 GLU cc_start: 0.9374 (mm-30) cc_final: 0.8976 (mt-10) REVERT: B 793 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8409 (pp20) REVERT: B 871 LYS cc_start: 0.8908 (mttt) cc_final: 0.8475 (pttp) REVERT: B 927 LEU cc_start: 0.6759 (OUTLIER) cc_final: 0.6488 (mt) REVERT: C 79 HIS cc_start: 0.8143 (m-70) cc_final: 0.7828 (m90) REVERT: C 238 PHE cc_start: 0.8957 (m-10) cc_final: 0.8713 (m-80) REVERT: D 141 MET cc_start: 0.8588 (mtt) cc_final: 0.8374 (mpp) REVERT: D 158 TYR cc_start: 0.7539 (m-80) cc_final: 0.7031 (m-80) REVERT: D 188 MET cc_start: -0.0759 (mmm) cc_final: -0.1688 (tpt) REVERT: D 323 GLU cc_start: 0.8755 (pm20) cc_final: 0.8292 (mp0) outliers start: 29 outliers final: 17 residues processed: 131 average time/residue: 0.2718 time to fit residues: 51.2540 Evaluate side-chains 128 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 1017 HIS Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 429 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 66 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 946 HIS ** B1017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 12749 Z= 0.334 Angle : 0.719 8.729 17632 Z= 0.388 Chirality : 0.044 0.208 1957 Planarity : 0.005 0.060 1931 Dihedral : 23.148 72.286 2484 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.63 % Favored : 95.29 % Rotamer: Outliers : 3.33 % Allowed : 14.76 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.23), residues: 1273 helix: -0.20 (0.21), residues: 577 sheet: -0.18 (0.61), residues: 71 loop : -0.63 (0.26), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1091 HIS 0.012 0.002 HIS B 919 PHE 0.033 0.003 PHE D 150 TYR 0.033 0.002 TYR B1000 ARG 0.004 0.001 ARG B 967 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 109 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 803 MET cc_start: 0.6159 (mtm) cc_final: 0.5015 (ttp) REVERT: A 826 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8698 (pp) REVERT: A 833 PHE cc_start: 0.9376 (m-80) cc_final: 0.9078 (m-80) REVERT: A 1040 PHE cc_start: 0.5978 (t80) cc_final: 0.5460 (t80) REVERT: A 1045 LEU cc_start: 0.6161 (OUTLIER) cc_final: 0.5469 (tp) REVERT: A 1068 LYS cc_start: 0.9236 (mptt) cc_final: 0.8878 (tmmt) REVERT: A 1104 PHE cc_start: 0.8453 (m-80) cc_final: 0.8071 (m-80) REVERT: A 1135 GLU cc_start: 0.9389 (mm-30) cc_final: 0.8985 (mt-10) REVERT: B 793 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8390 (pp20) REVERT: B 871 LYS cc_start: 0.9043 (mttt) cc_final: 0.8627 (pttp) REVERT: B 927 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6826 (mt) REVERT: C 79 HIS cc_start: 0.8184 (m-70) cc_final: 0.7880 (m90) REVERT: D 139 MET cc_start: 0.2328 (ppp) cc_final: 0.1702 (ppp) REVERT: D 158 TYR cc_start: 0.7382 (m-80) cc_final: 0.6978 (m-80) REVERT: D 178 MET cc_start: 0.8214 (mmm) cc_final: 0.7607 (mmm) REVERT: D 188 MET cc_start: -0.0333 (mmm) cc_final: -0.0968 (tpt) REVERT: D 310 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8380 (tt0) REVERT: D 323 GLU cc_start: 0.8767 (pm20) cc_final: 0.8351 (mp0) outliers start: 39 outliers final: 23 residues processed: 137 average time/residue: 0.2553 time to fit residues: 51.3071 Evaluate side-chains 128 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1012 ASP Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 970 HIS Chi-restraints excluded: chain B residue 1017 HIS Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 429 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 76 optimal weight: 0.0670 chunk 32 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 125 optimal weight: 0.3980 overall best weight: 0.8522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 946 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.5255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12749 Z= 0.219 Angle : 0.648 9.927 17632 Z= 0.351 Chirality : 0.041 0.210 1957 Planarity : 0.004 0.058 1931 Dihedral : 22.889 72.985 2484 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.75 % Favored : 97.17 % Rotamer: Outliers : 2.22 % Allowed : 16.81 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.23), residues: 1273 helix: 0.12 (0.21), residues: 576 sheet: -0.39 (0.55), residues: 84 loop : -0.48 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1008 HIS 0.009 0.001 HIS B 919 PHE 0.025 0.002 PHE D 150 TYR 0.027 0.002 TYR B1000 ARG 0.011 0.000 ARG A 784 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 803 MET cc_start: 0.6022 (mtm) cc_final: 0.5348 (ttp) REVERT: A 826 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8666 (pp) REVERT: A 830 TRP cc_start: 0.8422 (t60) cc_final: 0.8169 (t60) REVERT: A 833 PHE cc_start: 0.9355 (m-80) cc_final: 0.9053 (m-80) REVERT: A 872 MET cc_start: 0.4869 (ttm) cc_final: 0.4582 (mtp) REVERT: A 1040 PHE cc_start: 0.5847 (t80) cc_final: 0.5274 (t80) REVERT: A 1068 LYS cc_start: 0.9224 (mptt) cc_final: 0.8969 (pptt) REVERT: A 1104 PHE cc_start: 0.8298 (m-80) cc_final: 0.7853 (m-80) REVERT: A 1131 LYS cc_start: 0.8069 (mmmm) cc_final: 0.7487 (tmmt) REVERT: A 1135 GLU cc_start: 0.9315 (mm-30) cc_final: 0.8842 (mt-10) REVERT: A 1154 TYR cc_start: 0.7761 (p90) cc_final: 0.7509 (p90) REVERT: B 774 ARG cc_start: 0.8842 (mmp-170) cc_final: 0.8635 (mmp80) REVERT: B 793 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8352 (pp20) REVERT: B 871 LYS cc_start: 0.9005 (mttt) cc_final: 0.8579 (pttp) REVERT: B 927 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6720 (mt) REVERT: C 79 HIS cc_start: 0.8024 (m-70) cc_final: 0.7633 (m90) REVERT: C 166 PHE cc_start: 0.5397 (m-10) cc_final: 0.4673 (m-10) REVERT: D 139 MET cc_start: 0.2034 (ppp) cc_final: 0.1712 (ppp) REVERT: D 158 TYR cc_start: 0.7498 (m-80) cc_final: 0.7151 (m-80) REVERT: D 188 MET cc_start: -0.0337 (mmm) cc_final: -0.1457 (tpt) REVERT: D 310 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8389 (tt0) REVERT: D 323 GLU cc_start: 0.8765 (pm20) cc_final: 0.8307 (mp0) outliers start: 26 outliers final: 13 residues processed: 134 average time/residue: 0.2631 time to fit residues: 50.7036 Evaluate side-chains 122 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 970 HIS Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 429 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 95 optimal weight: 8.9990 chunk 73 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1114 GLN ** A1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 946 HIS B 959 GLN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.5556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12749 Z= 0.238 Angle : 0.661 9.734 17632 Z= 0.353 Chirality : 0.041 0.215 1957 Planarity : 0.004 0.060 1931 Dihedral : 22.731 71.560 2482 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.93 % Favored : 95.99 % Rotamer: Outliers : 2.39 % Allowed : 17.83 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.24), residues: 1273 helix: 0.16 (0.21), residues: 580 sheet: -0.54 (0.56), residues: 86 loop : -0.47 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1091 HIS 0.007 0.001 HIS B 919 PHE 0.029 0.002 PHE D 150 TYR 0.019 0.002 TYR B 945 ARG 0.010 0.000 ARG A1043 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 788 MET cc_start: 0.4895 (tpp) cc_final: 0.4554 (tpp) REVERT: A 803 MET cc_start: 0.6019 (mtm) cc_final: 0.5338 (ttp) REVERT: A 826 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8668 (pp) REVERT: A 827 LEU cc_start: 0.9025 (mt) cc_final: 0.8691 (mt) REVERT: A 830 TRP cc_start: 0.8454 (t60) cc_final: 0.8170 (t60) REVERT: A 833 PHE cc_start: 0.9370 (m-80) cc_final: 0.9089 (m-80) REVERT: A 1040 PHE cc_start: 0.5576 (t80) cc_final: 0.5020 (t80) REVERT: A 1045 LEU cc_start: 0.5765 (OUTLIER) cc_final: 0.4744 (tp) REVERT: A 1068 LYS cc_start: 0.9232 (mptt) cc_final: 0.9004 (pptt) REVERT: A 1104 PHE cc_start: 0.8356 (m-80) cc_final: 0.7923 (m-80) REVERT: A 1135 GLU cc_start: 0.9304 (mm-30) cc_final: 0.8902 (mt-10) REVERT: B 793 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8348 (pp20) REVERT: B 871 LYS cc_start: 0.9013 (mttt) cc_final: 0.8608 (pttp) REVERT: B 927 LEU cc_start: 0.7023 (OUTLIER) cc_final: 0.6779 (mt) REVERT: C 79 HIS cc_start: 0.8039 (m-70) cc_final: 0.7711 (m90) REVERT: C 166 PHE cc_start: 0.5294 (m-10) cc_final: 0.4554 (m-10) REVERT: D 158 TYR cc_start: 0.7596 (m-80) cc_final: 0.7247 (m-80) REVERT: D 178 MET cc_start: 0.8129 (mmm) cc_final: 0.7917 (mmm) REVERT: D 188 MET cc_start: -0.0217 (mmm) cc_final: -0.1337 (tpt) REVERT: D 310 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8411 (tt0) REVERT: D 323 GLU cc_start: 0.8765 (pm20) cc_final: 0.8345 (mp0) outliers start: 28 outliers final: 18 residues processed: 129 average time/residue: 0.2733 time to fit residues: 50.5587 Evaluate side-chains 127 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 914 LEU Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 1017 HIS Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 429 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 0.6980 chunk 77 optimal weight: 0.1980 chunk 39 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 82 optimal weight: 0.0020 chunk 88 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 12 optimal weight: 0.0470 chunk 102 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 chunk 124 optimal weight: 0.7980 overall best weight: 0.3286 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 946 HIS ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.5980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12749 Z= 0.187 Angle : 0.629 11.767 17632 Z= 0.341 Chirality : 0.040 0.202 1957 Planarity : 0.004 0.061 1931 Dihedral : 22.367 71.385 2482 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.59 % Favored : 97.33 % Rotamer: Outliers : 1.88 % Allowed : 18.09 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.24), residues: 1273 helix: 0.39 (0.21), residues: 579 sheet: -0.25 (0.59), residues: 80 loop : -0.36 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1008 HIS 0.008 0.001 HIS B 919 PHE 0.021 0.002 PHE B 739 TYR 0.029 0.002 TYR D 140 ARG 0.007 0.000 ARG A 784 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 788 MET cc_start: 0.5377 (tpp) cc_final: 0.5154 (tpp) REVERT: A 803 MET cc_start: 0.6044 (mtm) cc_final: 0.5420 (ttp) REVERT: A 826 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8586 (pp) REVERT: A 827 LEU cc_start: 0.9030 (mt) cc_final: 0.8703 (mt) REVERT: A 830 TRP cc_start: 0.8359 (t60) cc_final: 0.8112 (t60) REVERT: A 833 PHE cc_start: 0.9360 (m-80) cc_final: 0.9090 (m-80) REVERT: A 984 CYS cc_start: 0.8117 (t) cc_final: 0.7889 (p) REVERT: A 1040 PHE cc_start: 0.5154 (t80) cc_final: 0.4642 (t80) REVERT: A 1045 LEU cc_start: 0.5289 (OUTLIER) cc_final: 0.4293 (tp) REVERT: A 1068 LYS cc_start: 0.9183 (mptt) cc_final: 0.8979 (pptt) REVERT: A 1104 PHE cc_start: 0.8221 (m-80) cc_final: 0.7916 (m-80) REVERT: A 1131 LYS cc_start: 0.7789 (mmmm) cc_final: 0.7182 (tmmt) REVERT: A 1135 GLU cc_start: 0.9248 (mm-30) cc_final: 0.8775 (mt-10) REVERT: B 774 ARG cc_start: 0.8819 (mmp-170) cc_final: 0.8418 (ttp-110) REVERT: B 779 LYS cc_start: 0.8278 (mtpp) cc_final: 0.7975 (ttpp) REVERT: B 793 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8373 (pp20) REVERT: B 871 LYS cc_start: 0.8939 (mttt) cc_final: 0.8523 (pttp) REVERT: C 79 HIS cc_start: 0.7895 (m-70) cc_final: 0.7590 (m-70) REVERT: C 166 PHE cc_start: 0.5188 (m-10) cc_final: 0.4517 (m-10) REVERT: D 158 TYR cc_start: 0.7656 (m-80) cc_final: 0.7262 (m-80) REVERT: D 188 MET cc_start: -0.0393 (mmm) cc_final: -0.1280 (tpt) REVERT: D 323 GLU cc_start: 0.8753 (pm20) cc_final: 0.8329 (mp0) outliers start: 22 outliers final: 13 residues processed: 135 average time/residue: 0.2577 time to fit residues: 51.0608 Evaluate side-chains 121 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 429 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 8.9990 chunk 121 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 109 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 120 optimal weight: 0.4980 chunk 79 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1017 HIS ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.6159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12749 Z= 0.207 Angle : 0.645 11.238 17632 Z= 0.345 Chirality : 0.041 0.219 1957 Planarity : 0.004 0.064 1931 Dihedral : 22.314 70.951 2482 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.38 % Favored : 96.54 % Rotamer: Outliers : 1.45 % Allowed : 18.43 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.24), residues: 1273 helix: 0.45 (0.22), residues: 579 sheet: -0.24 (0.59), residues: 80 loop : -0.28 (0.27), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 93 HIS 0.009 0.001 HIS B 919 PHE 0.027 0.002 PHE D 150 TYR 0.041 0.002 TYR D 140 ARG 0.006 0.000 ARG A 784 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 788 MET cc_start: 0.5647 (tpp) cc_final: 0.5432 (tpp) REVERT: A 803 MET cc_start: 0.6077 (mtm) cc_final: 0.5415 (ttp) REVERT: A 826 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8629 (pp) REVERT: A 827 LEU cc_start: 0.9036 (mt) cc_final: 0.8708 (mt) REVERT: A 830 TRP cc_start: 0.8403 (t60) cc_final: 0.8142 (t60) REVERT: A 833 PHE cc_start: 0.9379 (m-80) cc_final: 0.9117 (m-80) REVERT: A 984 CYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7880 (p) REVERT: A 1040 PHE cc_start: 0.5133 (t80) cc_final: 0.4603 (t80) REVERT: A 1045 LEU cc_start: 0.5179 (OUTLIER) cc_final: 0.4225 (tp) REVERT: A 1104 PHE cc_start: 0.8251 (m-80) cc_final: 0.7816 (m-80) REVERT: A 1131 LYS cc_start: 0.7932 (mmmm) cc_final: 0.7335 (tmmt) REVERT: A 1135 GLU cc_start: 0.9252 (mm-30) cc_final: 0.8788 (mt-10) REVERT: B 779 LYS cc_start: 0.8305 (mtpp) cc_final: 0.8018 (ttpp) REVERT: B 871 LYS cc_start: 0.8961 (mttt) cc_final: 0.8561 (pttp) REVERT: C 79 HIS cc_start: 0.7947 (m-70) cc_final: 0.7576 (m90) REVERT: D 158 TYR cc_start: 0.7654 (m-80) cc_final: 0.7256 (m-80) REVERT: D 188 MET cc_start: -0.1295 (mmm) cc_final: -0.1862 (tpt) REVERT: D 323 GLU cc_start: 0.8681 (pm20) cc_final: 0.8258 (mp0) outliers start: 17 outliers final: 14 residues processed: 120 average time/residue: 0.2709 time to fit residues: 46.7404 Evaluate side-chains 120 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1017 HIS Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 429 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 8.9990 chunk 78 optimal weight: 0.2980 chunk 60 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 134 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 82 optimal weight: 0.0170 chunk 65 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 925 GLN B1017 HIS ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.6391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12749 Z= 0.194 Angle : 0.660 11.106 17632 Z= 0.352 Chirality : 0.042 0.212 1957 Planarity : 0.004 0.063 1931 Dihedral : 22.197 70.324 2482 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.22 % Favored : 96.70 % Rotamer: Outliers : 1.79 % Allowed : 18.52 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.24), residues: 1273 helix: 0.56 (0.22), residues: 579 sheet: -0.56 (0.61), residues: 71 loop : -0.26 (0.26), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 93 HIS 0.008 0.001 HIS B 919 PHE 0.022 0.002 PHE D 150 TYR 0.043 0.001 TYR D 140 ARG 0.010 0.000 ARG B 774 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 803 MET cc_start: 0.6041 (mtm) cc_final: 0.5383 (ttp) REVERT: A 826 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8624 (pp) REVERT: A 827 LEU cc_start: 0.9040 (mt) cc_final: 0.8715 (mt) REVERT: A 830 TRP cc_start: 0.8372 (t60) cc_final: 0.8117 (t60) REVERT: A 833 PHE cc_start: 0.9380 (m-80) cc_final: 0.9117 (m-80) REVERT: A 984 CYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7878 (p) REVERT: A 1040 PHE cc_start: 0.4891 (t80) cc_final: 0.4082 (t80) REVERT: A 1045 LEU cc_start: 0.5053 (OUTLIER) cc_final: 0.4107 (tp) REVERT: A 1104 PHE cc_start: 0.8208 (m-80) cc_final: 0.7899 (m-80) REVERT: A 1131 LYS cc_start: 0.7773 (mmmm) cc_final: 0.7142 (tmmt) REVERT: A 1135 GLU cc_start: 0.9265 (mm-30) cc_final: 0.8805 (mt-10) REVERT: B 774 ARG cc_start: 0.9124 (mmp80) cc_final: 0.8790 (ttp-110) REVERT: B 779 LYS cc_start: 0.8244 (mtpp) cc_final: 0.7958 (ttpp) REVERT: B 871 LYS cc_start: 0.8918 (mttt) cc_final: 0.8508 (pttp) REVERT: C 79 HIS cc_start: 0.7881 (m-70) cc_final: 0.7476 (m90) REVERT: D 158 TYR cc_start: 0.7638 (m-80) cc_final: 0.7226 (m-80) REVERT: D 188 MET cc_start: -0.0990 (mmm) cc_final: -0.1428 (tpt) REVERT: D 323 GLU cc_start: 0.8646 (pm20) cc_final: 0.8111 (mp0) outliers start: 21 outliers final: 14 residues processed: 119 average time/residue: 0.2658 time to fit residues: 46.1148 Evaluate side-chains 120 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1017 HIS Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 429 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 20.0000 chunk 32 optimal weight: 0.0770 chunk 98 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 13 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 overall best weight: 1.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.124308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.099159 restraints weight = 57024.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.102123 restraints weight = 29507.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.103939 restraints weight = 19189.692| |-----------------------------------------------------------------------------| r_work (final): 0.4426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6024 moved from start: 0.6479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12749 Z= 0.221 Angle : 0.675 13.563 17632 Z= 0.354 Chirality : 0.042 0.232 1957 Planarity : 0.004 0.064 1931 Dihedral : 22.168 69.916 2482 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.53 % Favored : 96.39 % Rotamer: Outliers : 1.28 % Allowed : 19.37 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.24), residues: 1273 helix: 0.55 (0.22), residues: 580 sheet: -0.59 (0.58), residues: 84 loop : -0.23 (0.27), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 93 HIS 0.009 0.001 HIS B 970 PHE 0.024 0.002 PHE D 150 TYR 0.038 0.002 TYR D 140 ARG 0.011 0.000 ARG B 774 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2661.48 seconds wall clock time: 49 minutes 46.57 seconds (2986.57 seconds total)